//------------------------------//
// The Answer 2 
// Story: Life is a Test: A Series of Pony Logic Puzzles 
// by Brony_of_Brody 
//------------------------------//

Although each pony arrived at different times, the train departure times were all fixed, and not evenly spaced out either.

You would expect a reasonably even number if each train departures were all evenly spaced out. But they weren't, and Trixie didn't think about this. 

Imagine a scenario where there was only one train to each destination per day. For example, one Las Pegasus train was at 10:00, a San Diegoat train was at 11:36 and a Manehatten train was at 14:00. If  you arrived between 14:00 and 10:00 THE FOLLOWING DAY, it means that the first train to catch would be the one going to Las Pegasus at 10:00.

So there'd be a 20/24 chance of going to Las Pegasus (hence why 25 ponies wound up there), a 3/30 chance of going to Manehatten, and a 2/30 chance of going to San Diegoat.